The figures, provided to The Age by Public Transport Victoria, indicate the state's public transport system is treading water at best, and continues to struggle to provide a reliable service for the millions who use it, despite renewed political focus on reversing decades of system neglect.

The Andrews government made public transport a centrepiece of its 2014 election platform, but has focused its efforts on major projects that will not bear fruit for several years - removing 50 level crossings by 2022 and planning to build the Melbourne Metro rail tunnel by 2026.

Overall, Metro ran 92.5 per cent of trains on time last year, down from 92.8 per cent in 2014.

The worst lines, with less than 90 per cent punctuality, were all in the south-east: the Cranbourne, Pakenham and Frankston lines. The Frankston line languished despite a $115 million upgrade by the former Napthine government.

Metro has set itself a target of running 95 per cent of trains on time, but that mark has moved further out of reach.

Spokeswoman Sammie Black defended the operator's performance, saying the small drop in punctuality happened in a year when patronage rose 3.1 per cent.

"We have continued to provide a strong performance which has exceeded franchise targets," Ms Black said.

"We will continue to work with government to deliver more punctual services, more often for our customers across all lines."

A Metro service is considered on time if it reaches its destination four minutes and 59 seconds behind schedule. Metro must run 88 per cent of trains on time to adhere to performance standards in its franchise agreement with the state government.

The generous performance standards are expected to be toughened when the rail franchise agreement expires in 2017.

"Both the Labor and Liberal parties have neglected public transport for too long," he said. "The problems which cause trains to run late can be fixed, but the government doesn't have a plan."

The Greens want a switch to contemporary signalling technology to increase capacity and improve punctuality.

"Cities around the world are benefiting from digital signals while we are left with an old and unreliable system which just isn't up to the job," Mr Barber said.

Tram passengers fared even worse than train passengers in 2015. Yarra Trams' punctuality slipped from 83.9 per cent to 82.6 per cent.

Just two routes - route 75 between Docklands and Vermont South and the minor route 78 between North Richmond and Balaclava - were more on time in 2015 than in 2014.

Yarra Trams spokesman Simon Murphy said tram punctuality had been affected by the popularity of the free tram zone, a large number of special events such as the Australian Open and White Night, and a series of works to build platform tram stops.

"Tram punctuality has been trending upwards since 2010, with 2014 being a record-breaking year," Mr Murphy said.

"The punctuality result for 2015 is more in line with the overall upward trend we have seen over the last five years."

V/Line's on-time performance increased from 87.8 per cent in 2014 to 88.6 last year.

Gippsland trains made the biggest gains, from 79.2 per cent to 82.6 per cent of services. The Geelong and Bendigo lines made minor gains, while performance on the Ballarat and Seymour lines declined.

Spokeswoman Ebony Jordan said V/Line was pleased to have run more trains on time last year.

This had been achieved in part through a maintenance program that removed the need for many temporary speed restrictions on regional tracks.